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g_sorient_d

NAME

g_sorient - analyzes solvent orientation around solutes

SYNOPSIS

g_sorient -f traj.xtc -s topol.tpr -n index.ndx -o sori.xvg -no snor.xvg -ro sord.xvg -co scum.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -[no]com -rmin real -rmax real -bin real -[no]pbc

DESCRIPTION

g_sorient analyzes solvent orientation around solutes. It calculates two angles between the vector from one or more reference positions to the first atom of each solvent molecule: theta1: the angle with the vector from the first atom of the solvent molecule to the midpoint between atoms 2 and 3.

theta2: the angle with the normal of the solvent plane, defined by the same three atoms.

The reference can be a set of atoms or the center of mass of a set of atoms. The group of solvent atoms should consist of 3 atoms per solvent molecule. Only solvent molecules between -rmin and -rmax are considered for -o and -no each frame.

-o : distribtion of cos(theta1) for rmin=r=rmax.

-no : distribution of 3cos2(theta2)-1 for rmin=r=rmax.

-ro : cos(theta1) and 3cos2(theta2)-1 as a function of the distance.

-co : the sum over all solvent molecules within distance r of cos(theta1) and 3cos2(theta2)-1 as a function of r.

FILES

-f traj.xtc Input
 Generic trajectory: xtc trr trj gro g96 pdb 

-s topol.tpr Input
 Structure+mass(db): tpr tpb tpa gro g96 pdb xml 

-n index.ndx Input, Opt.
 Index file 

-o sori.xvg Output
 xvgr/xmgr file 

-no snor.xvg Output
 xvgr/xmgr file 

-ro sord.xvg Output
 xvgr/xmgr file 

-co scum.xvg Output
 xvgr/xmgr file 

OTHER OPTIONS

-[no]h no
 Print help info and quit

-nice int 19
 Set the nicelevel

-b time 0
 First frame (ps) to read from trajectory

-e time 0
 Last frame (ps) to read from trajectory

-dt time 0
 Only use frame when t MOD dt = first time (ps)

-[no]w no
 View output xvg, xpm, eps and pdb files

-[no]xvgr yes
 Add specific codes (legends etc.) in the output xvg files for the xmgrace program

-[no]com no
 Use the center of mass as the reference postion

-rmin real 0
 Minimum distance

-rmax real 0.5
 Maximum distance

-bin real 0.02
 Binwidth

-[no]pbc no
 Check PBC for the center of mass calculation. Only necessary when your reference group consists of several molecules.

SEE ALSO

gromacs(7)

More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.